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cache epsilon computations for MPB to improve MPI scaling #1257

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Jun 26, 2020
Merged

cache epsilon computations for MPB to improve MPI scaling #1257

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c6aca70
cache epsilon computations for MPB to improve MPI scaling
stevengj Jun 19, 2020
158882a
whoops
stevengj Jun 19, 2020
6d4d772
tweak
stevengj Jun 19, 2020
ddb2337
fixes
stevengj Jun 20, 2020
85981c2
add missing sizeof
stevengj Jun 24, 2020
98ea4e4
tell MPB not to do its own subpixel averaging
stevengj Jun 24, 2020
32893d3
assert.h
stevengj Jun 25, 2020
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102 changes: 76 additions & 26 deletions src/mpb.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -41,35 +41,64 @@ typedef struct {
double frequency;
ndim dim;
const fields *f;

/* for parallel efficiency, we first cache the epsinv data from each process, then
sum_to_all to synchonize, and then re-run set_maxwell_dielectric with the cached data */
double *cache; // array of 6*ncache eps_inv matrix entries in the order that they are needed
size_t ncache; // allocated size of the cache
size_t icache; // current position in the cache
bool use_cache; // whether we are using the cache
} meep_mpb_eps_data;

static void meep_mpb_eps(symmetric_matrix *eps, symmetric_matrix *eps_inv, const mpb_real r[3],
static int meep_mpb_eps(symmetric_matrix *eps, symmetric_matrix *eps_inv,
mpb_real n[3], mpb_real d1, mpb_real d2, mpb_real d3, mpb_real tol,
const mpb_real r[3],
void *eps_data_) {
meep_mpb_eps_data *eps_data = (meep_mpb_eps_data *)eps_data_;
const double *s = eps_data->s;
const double *o = eps_data->o;
double frequency = eps_data->frequency;
vec p(eps_data->dim == D3 ? vec(o[0] + r[0] * s[0], o[1] + r[1] * s[1], o[2] + r[2] * s[2])
: (eps_data->dim == D2 ? vec(o[0] + r[0] * s[0], o[1] + r[1] * s[1]) :
/* D1 */ vec(o[2] + r[2] * s[2])));
const fields *f = eps_data->f;

eps_inv->m00 = real(f->get_chi1inv(Ex, X, p, frequency));
eps_inv->m11 = real(f->get_chi1inv(Ey, Y, p, frequency));
eps_inv->m22 = real(f->get_chi1inv(Ez, Z, p, frequency));

ASSIGN_ESCALAR(eps_inv->m01, real(f->get_chi1inv(Ex, Y, p, frequency)), 0);
ASSIGN_ESCALAR(eps_inv->m02, real(f->get_chi1inv(Ex, Z, p, frequency)), 0);
ASSIGN_ESCALAR(eps_inv->m12, real(f->get_chi1inv(Ey, Z, p, frequency)), 0);
/*
master_printf("m11(%g,%g) = %g\n", p.x(), p.y(), eps_inv->m00);
master_printf("m22(%g,%g) = %g\n", p.x(), p.y(), eps_inv->m11);
master_printf("m33(%g,%g) = %g\n", p.x(), p.y(), eps_inv->m22);
master_printf("m12(%g,%g) = %g\n", p.x(), p.y(), eps_inv->m01);
master_printf("m13(%g,%g) = %g\n", p.x(), p.y(), eps_inv->m02);
master_printf("m23(%g,%g) = %g\n", p.x(), p.y(), eps_inv->m12);
*/
maxwell_sym_matrix_invert(eps, eps_inv);
size_t i = eps_data->icache;

(void) n; (void) d1; (void) d2; (void) d3; (void) tol; // unused

if (eps_data->use_cache) {
const double *cache = eps_data->cache;
eps_inv->m00 = cache[6*i];
eps_inv->m11 = cache[6*i+1];
eps_inv->m22 = cache[6*i+2];
ASSIGN_ESCALAR(eps_inv->m01, cache[6*i+3], 0);
ASSIGN_ESCALAR(eps_inv->m02, cache[6*i+4], 0);
ASSIGN_ESCALAR(eps_inv->m12, cache[6*i+5], 0);
maxwell_sym_matrix_invert(eps, eps_inv);
}
else {
// get cache pointer, doubling cache size as needed:
double *cache = i < eps_data->ncache ? eps_data->cache :
(eps_data->cache = (double*) realloc(eps_data->cache, sizeof(double) * 6 * (eps_data->ncache *= 2)));

const double *s = eps_data->s;
const double *o = eps_data->o;
double frequency = eps_data->frequency;
vec p(eps_data->dim == D3 ? vec(o[0] + r[0] * s[0], o[1] + r[1] * s[1], o[2] + r[2] * s[2])
: (eps_data->dim == D2 ? vec(o[0] + r[0] * s[0], o[1] + r[1] * s[1]) :
/* D1 */ vec(o[2] + r[2] * s[2])));
const fields *f = eps_data->f;

// call get_chi1inv with parallel=false to get only local epsilon data
cache[6*i] = real(f->get_chi1inv(Ex, X, p, frequency, false));
cache[6*i+1] = real(f->get_chi1inv(Ey, Y, p, frequency, false));
cache[6*i+2] = real(f->get_chi1inv(Ez, Z, p, frequency, false));
cache[6*i+3] = real(f->get_chi1inv(Ex, Y, p, frequency, false));
cache[6*i+4] = real(f->get_chi1inv(Ex, Z, p, frequency, false));
cache[6*i+5] = real(f->get_chi1inv(Ey, Z, p, frequency, false));

// return a dummy value epsilon = 1 while we are building up the cache
eps->m00 = eps->m11 = eps->m22 = eps_inv->m00 = eps_inv->m11 = eps_inv->m22 = 1;
ASSIGN_ESCALAR(eps->m01, 0, 0);
eps->m02 = eps->m12 = eps_inv->m01 = eps_inv->m02 = eps_inv->m12 = eps->m01;
}

eps_data->icache += 1; // next call will use the subsequent cache element

return 1; // tells MPB not to do its own subpixel averaging
}

/**************************************************************/
Expand Down Expand Up @@ -382,7 +411,28 @@ void *fields::get_eigenmode(double frequency, direction d, const volume where, c
eps_data.dim = gv.dim;
eps_data.f = this;
eps_data.frequency = frequency;
set_maxwell_dielectric(mdata, mesh_size, R, G, meep_mpb_eps, NULL, &eps_data);
eps_data.cache = (double *) malloc(sizeof(double) * 6 * (eps_data.ncache = 512));

// first, build up a cache of the local epsilon data (while returning dummy values to MPB)
eps_data.use_cache = false;
eps_data.icache = 0;
set_maxwell_dielectric(mdata, mesh_size, R, G, NULL, meep_mpb_eps, &eps_data);

// then, synchronize the data
eps_data.ncache = eps_data.icache; // actual amount of cached data
double *summed_cache = (double *) malloc(sizeof(double) * 6 * eps_data.ncache);
sum_to_all(eps_data.cache, summed_cache, eps_data.ncache*6);
free(eps_data.cache);
eps_data.cache = summed_cache;

// finally, send MPB the real epsilon data using the synchronized cache
eps_data.use_cache = true;
eps_data.icache = 0;
set_maxwell_dielectric(mdata, mesh_size, R, G, NULL, meep_mpb_eps, &eps_data);
assert(eps_data.icache == eps_data.ncache);
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free(eps_data.cache);

if (user_mdata) *user_mdata = (void *)mdata;
}
else {
Expand Down